Summary

An account
on the computer cluster with PBS support (for example, VPAC username,
password)

This document is written by Yongli Ren, TULIP Lab . With some resource is taken from VPAC
Tutorial Website and the README file for Linux published with Matlab.

Submit Matlab Jobs to VPAC on Linux

1. Set up SSH on
linux.

Run
the following commands in order: ssh-keygen, ssh-copy-id user@tango.vpac.org %% replacing user
with your own VPAC account, and ssh-add. This step is shown in
Figure 1.

Figure 1. Set up SSH

After that, you will set up a
passwordless ssh where you can access to VPAC without password
requirement. This step is vital, because Matlab needs this passwordless
ssh configuration to submit jobs to VPAC. You can check this by running
command:ssh
user@tango.vpac.org %%% replacing user
with your own VPAC account.If you can access to VPAC without any
password requirement, you succeed in this step.

2. Set up Matlab
working environment at local host.

At this step, it would be easy for
Windows user, but for Linux user, it would be a little bit tricky, since
Linux is a multi-user system. For some Linux users, they prefer to
install softwares with the root account, which is a good habit but may
cause some problems for changing those software’s environment manually.
For instance, if you installed Matlab with Root account, you will not be
able to change files or paths in Matlab folder with your working
account. This would put some difficulties in this step. But no worries,
we can figure out one way to solve those problems.

a). In Matoab is
toolbox, there is a one that is vital for VPAC job submission. It is the
“distcomp” folder:

$MATLABROOT/toolbox/distcomp

Copy this “distcomp”
folder to a new folder which is created with your working account. Then,
we can start from there, since you have all the permission for the
newly created folders. More importantly, add the new folder and its
subfolders in Matlab’s path. We will use $distcomp represent where you
create the new “distcomp” folder.

b). Go to folder:
$distcomp/@distcomp/@abstractscheduler

Rename pGetJobState.m to
OLD_pGetJobState.m_OLD and pDestroyJob.m toOLD_pDestroyJob.m_OLD.
or you can directly delete these two files.

c). Copy

$distcomp/examples/integration/pbs/nonshared/unix/pGetJobState.mand place it in$distcomp/@distcomp/@abstractscheduler/

d). Copy

$distcomp/examples/integration/pbs/nonshared/unix/pDestroyJob.mand place it in$distcomp/@distcomp/@abstractscheduler/

3. Copy new submit
function from VPAC to the local host.

Since the standard Parallel and Simple
Submit Functions have been modified by VPAC. So we need to copy two more
files from VPAC: Copy pbsNonSharedParallelSubmitFcn.m and
pbsNonSharedSimpleSubmitFcn.m, on tango.vpac.org from:
/common/examples/matlab To $distcomp/examples/integration/pbs/nonshared/unix

4. Finally, once
again, please NOTE: The account name you use to run Matlab on Linux
should be exactly the same as the one you have for VPAC, namely your
VPAC account. You can run “whoami” command: